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@charles-cowart
charles-cowart committed Nov 7, 2024
1 parent 09a1cc2 commit 73d5d06
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56 changes: 40 additions & 16 deletions qp_klp/SequencingTech.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,17 @@ class TellSeq(SequencingTech):
seqtech_type = SEQTECH_NAME_TELLSEQ

def convert_raw_to_fastq(self):
config = self.pipeline.get_software_configuration('tell-read')
# NB: Note that 'tell-seq' currently encapsulates the parameters
# for all sub-tasks including tell-read, integrate, etc. Some of
# these tasks may have different values for parameters like
# 'cores_per_task'. When differences are encountered, please create
# separate values for each in the tell-seq section.
config = self.pipeline.get_software_configuration('tell-seq')

print("RUN DIR: %s" % self.pipeline.run_dir)
print("OUTPUT PATH: %s" % self.pipeline.output_path)
print("INPUT FILE PATH: %s" % self.pipeline.input_file_path)
print("CONFIG: %s" % config)

tr_job = TellReadJob(self.pipeline.run_dir,
self.pipeline.output_path,
Expand All @@ -106,28 +112,16 @@ def convert_raw_to_fastq(self):
config['label'],
config['reference_base'],
config['reference_map'],
config['tmp1_path'],
config['sing_script_path'],
config['cores_per_task'])

tr_job.run(callback=self.status_update_callback)

'''
when run is run, we're going to create a job script which we can test to see if it checks out.
then we're going to submit the job, and we need to fake the sbatch command.
then we need to fake the results directory.
all we're testing is that the job script is what we expect.
'''

"""
# TODO: determine these appropriately
max_array_length = "foo"
label = "bar"

if self.iseq_run:
print("PERFORMING NCJOB")
# NB: the original master script performed this job prior to
# integration and after the main job completed, but only
# for iSeq jobs. This may be useful for additional
Expand All @@ -146,6 +140,12 @@ def convert_raw_to_fastq(self):
label)

nc_job.run(callback=self.status_update_callback)
else:
print("SKIPPING NCJOB")

# TODO: Replace these hardcodes
reference_base = ""
reference_map = ""

# after the primary job and the optional counts job is completed,
# the job to integrate results and add metadata to the fastq files
Expand All @@ -161,10 +161,35 @@ def convert_raw_to_fastq(self):
self.master_qiita_job_id,
max_array_length,
config['indicies_script_path'],
label)
label,
reference_base,
reference_map,
config['cores_per_task'])

i_job.run(callback=self.status_update_callback)

print("DONE WITH INTEGRATE JOB")

fake_audit_results = []

return fake_audit_results

# we need to return back what failed to process

'''
when run is run, we're going to create a job script which we can test to see if it checks out.
then we're going to submit the job, and we need to fake the sbatch command.
then we need to fake the results directory.
all we're testing is that the job script is what we expect.
'''

"""
# TODO: determine these appropriately
# NB: after i_job is completed, there are two optional jobs that
# can be performed in parallel using the new functionality in Job()
# class. However we are not using the output from this step right now
Expand Down Expand Up @@ -234,7 +259,6 @@ def convert_raw_to_fastq(self):
\
def _post_process_file(self, fastq_file, mapping):
# generate names of the form generated by bcl-convert/bcl2fastq:
Expand Down
3 changes: 3 additions & 0 deletions qp_klp/Workflows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1195,6 +1195,9 @@ class TellSeqMetagenomicWorkflow(Workflow, Metagenomic, TellSeq):
def __init__(self, **kwargs):
super().__init__(**kwargs)

# TODO: For now set to False
self.iseq_run = False

# TODO: Replace these with frozen set() or similar.
self.mandatory_attributes = ['qclient', 'uif_path', 'config_fp',
'run_identifier', 'output_dir', 'job_id',
Expand Down
4 changes: 2 additions & 2 deletions qp_klp/tests/data/configuration_profiles/miseq_metagenomic.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,10 @@
"instrument_type": "MiSeq",
"assay_type": "Metagenomic",
"configuration": {
"tell-read": {
"tell-seq": {
"label": "my_label",
"reference_base": "/my/reference/base/path",
"reference_map": "/my/reference/map/path",
"tmp1_path": "/my/tmp1/path",
"sing_script_path": "/my/sing/script/path",
"cores_per_task": "999",
"nodes": 1,
Expand All @@ -17,6 +16,7 @@
"modules_to_load": [
"foo_module"
],
"indicies_script_path": "my/indicies/script/path",
"per_process_memory_limit": "10"
},
"bcl-convert": {
Expand Down
95 changes: 3 additions & 92 deletions qp_klp/tests/data/sample-sheets/metagenomic/tellseq/good_sheet_draft1.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -17,102 +17,13 @@ Chemistry,Default,,,,,,,
ReverseComplement,0,,,,,,,
[Data],,,,,,,,
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,barcode_id,Sample_Project,Well_description,Lane,
LS_8_10_2013_SRE,LS.8.10.2013.SRE,LS_Donor_SS_Samples_P1,A1,C501,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.10.2013.SRE,4,
LS_12_17_2014_SRE,LS.12.17.2014.SRE,LS_Donor_SS_Samples_P1,B1,C509,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.17.2014.SRE,4,
LS_4_4_2015_SRE,LS.4.4.2015.SRE,LS_Donor_SS_Samples_P1,C1,C502,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.4.2015.SRE,4,
LS_2_23_2015_SRE,LS.2.23.2015.SRE,LS_Donor_SS_Samples_P1,D1,C510,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.23.2015.SRE,4,
LS_9_28_2014_SRE,LS.9.28.2014.SRE,LS_Donor_SS_Samples_P1,E1,C503,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.9.28.2014.SRE,4,
LS_12_14_2013_SRE,LS.12.14.2013.SRE,LS_Donor_SS_Samples_P1,F1,C511,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.14.2013.SRE,4,
LS_4_7_2013_SRE,LS.4.7.2013.SRE,LS_Donor_SS_Samples_P1,G1,C504,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.7.2013.SRE,4,
LS_7_14_2013_SRE,LS.7.14.2013.SRE,LS_Donor_SS_Samples_P1,H1,C512,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.14.2013.SRE,4,
LS_10_27_2013_SRE,LS.10.27.2013.SRE,LS_Donor_SS_Samples_P1,I1,C505,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.10.27.2013.SRE,4,
LS_1_19_2014_SRE,LS.1.19.2014.SRE,LS_Donor_SS_Samples_P1,J1,C513,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.19.2014.SRE,4,
LS_9_3_2013_SRE,LS.9.3.2013.SRE,LS_Donor_SS_Samples_P1,K1,C506,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.9.3.2013.SRE,4,
LS_2_25_2013_SRE,LS.2.25.2013.SRE,LS_Donor_SS_Samples_P1,L1,C514,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.25.2013.SRE,4,
LS_7_26_2015_SRE,LS.7.26.2015.SRE,LS_Donor_SS_Samples_P1,M1,C507,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.26.2015.SRE,4,
LS_2_17_2014_SRE,LS.2.17.2014.SRE,LS_Donor_SS_Samples_P1,N1,C515,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.17.2014.SRE,4,
LS_6_29_2015_SRE,LS.6.29.2015.SRE,LS_Donor_SS_Samples_P1,O1,C508,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.29.2015.SRE,4,
LS_3_24_2015_SRE,LS.3.24.2015.SRE,LS_Donor_SS_Samples_P1,P1,C516,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.24.2015.SRE,4,
LS_1_6_2015_SRE,LS.1.6.2015.SRE,LS_Donor_SS_Samples_P1,A2,C517,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.6.2015.SRE,4,
T_LS_7_15_15B_SRE,T.LS.7.15.15B.SRE,LS_Donor_SS_Samples_P1,B2,C525,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.15.15B.SRE,4,
LS_6_9_2013_SRE,LS.6.9.2013.SRE,LS_Donor_SS_Samples_P1,C2,C518,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.9.2013.SRE,4,
Person_A_SRE,Person_A.SRE,LS_Donor_SS_Samples_P1,D2,C526,Tellseq_Shortread_Metagenomic_Analysis_10283,Person_A.SRE,4,
LS_8_22_2014_R2_SRE,LS.8.22.2014.R2.SRE,LS_Donor_SS_Samples_P1,E2,C519,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.22.2014.R2.SRE,4,
Person_B_SRE,Person_B.SRE,LS_Donor_SS_Samples_P1,F2,C527,Tellseq_Shortread_Metagenomic_Analysis_10283,Person_B.SRE,4,
LS_8_22_2014_R1_SRE,LS.8.22.2014.R1.SRE,LS_Donor_SS_Samples_P1,G2,C520,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.22.2014.R1.SRE,4,
Person_C_SRE,Person_C.SRE,LS_Donor_SS_Samples_P1,H2,C528,Tellseq_Shortread_Metagenomic_Analysis_10283,Person_C.SRE,4,
LS_12_28_2011_SRE,LS.12.28.2011.SRE,LS_Donor_SS_Samples_P1,I2,C521,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.28.2011.SRE,4,
Person_D_SRE,Person_D.SRE,LS_Donor_SS_Samples_P1,J2,C529,Tellseq_Shortread_Metagenomic_Analysis_10283,Person_D.SRE,4,
LS_5_4_2014_SRE,LS.5.4.2014.SRE,LS_Donor_SS_Samples_P1,K2,C522,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.5.4.2014.SRE,4,
45208_1_1,45208.1.1,UROBIOME_TEST_MF_SAMPLES_P2,L2,C530,Tellseq_Shortread_Metagenomic_Analysis_10283,45208.1.1,4,
LS_11_6_2012_SRE,LS.11.6.2012.SRE,LS_Donor_SS_Samples_P1,M2,C523,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.11.6.2012.SRE,4,
45248_2_2,45248.2.2,UROBIOME_TEST_MF_SAMPLES_P2,N2,C531,Tellseq_Shortread_Metagenomic_Analysis_10283,45248.2.2,4,
LS_4_3_2012_SRE,LS.4.3.2012.SRE,LS_Donor_SS_Samples_P1,O2,C524,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.3.2012.SRE,4,
45261_2_1,45261.2.1,UROBIOME_TEST_MF_SAMPLES_P2,P2,C532,Tellseq_Shortread_Metagenomic_Analysis_10283,45261.2.1,4,
45272_11_2,45272.11.2,UROBIOME_TEST_MF_SAMPLES_P2,A3,C533,Tellseq_Shortread_Metagenomic_Analysis_10283,45272.11.2,4,
T_LS_7_12_15A,T.LS.7.12.15A,Larry_Smarr_Plus_Donor_Samples_P3,B3,C541,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.12.15A,4,
45316_8_1,45316.8.1,UROBIOME_TEST_MF_SAMPLES_P2,C3,C534,Tellseq_Shortread_Metagenomic_Analysis_10283,45316.8.1,4,
T_LS_7_8_15A,T.LS.7.8.15A,Larry_Smarr_Plus_Donor_Samples_P3,D3,C542,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.8.15A,4,
45327_7_2,45327.7.2,UROBIOME_TEST_MF_SAMPLES_P2,E3,C535,Tellseq_Shortread_Metagenomic_Analysis_10283,45327.7.2,4,
LS_8_10_2013,LS.8.10.2013,LS_Time_Series_ABSQ_P4,F3,C543,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.10.2013,4,
45272_1_swab_2,45272.1.swab.2,UROBIOME_TEST_MF_SAMPLES_P2,G3,C536,Tellseq_Shortread_Metagenomic_Analysis_10283,45272.1.swab.2,4,
LS_6_29_2015,LS.6.29.2015,LS_Time_Series_ABSQ_P4,H3,C544,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.29.2015,4,
45326_1_swab_2,45326.1.swab.2,UROBIOME_TEST_MF_SAMPLES_P2,I3,C537,Tellseq_Shortread_Metagenomic_Analysis_10283,45326.1.swab.2,4,
LS_3_8_2015,LS.3.8.2015,LS_Time_Series_ABSQ_P4,J3,C545,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.8.2015,4,
T_LS_7_19_15A,T.LS.7.19.15A,Larry_Smarr_Plus_Donor_Samples_P3,K3,C538,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.19.15A,4,
LS_4_29_2013,LS.4.29.2013,LS_Time_Series_ABSQ_P4,L3,C546,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.29.2013,4,
T_LS_7_15_15B,T.LS.7.15.15B,Larry_Smarr_Plus_Donor_Samples_P3,M3,C539,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.15.15B,4,
LS_11_16_2014,LS.11.16.2014,LS_Time_Series_ABSQ_P4,N3,C547,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.11.16.2014,4,
T_LS_7_19_15B,T.LS.7.19.15B,Larry_Smarr_Plus_Donor_Samples_P3,O3,C540,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.19.15B,4,
LS_1_19_2014,LS.1.19.2014,LS_Time_Series_ABSQ_P4,P3,C548,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.19.2014,4,
LS_3_24_2015,LS.3.24.2015,LS_Time_Series_ABSQ_P4,A4,C549,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.24.2015,4,
LS_2_8_2013,LS.2.8.2013,LS_Time_Series_ABSQ_P4,B4,C557,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.8.2013,4,
BLANK_K15_cancer_patient,BLANK.K15.cancer.patient,Tumor_Community_P7,F6,C591,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.K15.cancer.patient,4,
LS_11_10_2013,LS.11.10.2013,LS_Time_Series_ABSQ_P4,C4,C550,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.11.10.2013,4,
Marine_Sediment_0_2cm_R1,Marine.Sediment.0.2cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,D4,C558,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.0.2cm.R1,4,
LS_3_23_2014,LS.3.23.2014,LS_Time_Series_ABSQ_P4,E4,C551,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.23.2014,4,
Marine_Sediment_5_7cm_R1,Marine.Sediment.5.7cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,F4,C559,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.5.7cm.R1,4,
LS_1_14_2015,LS.1.14.2015,LS_Time_Series_ABSQ_P4,G4,C552,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.14.2015,4,
Marine_Sediment_10_12cm_R2,Marine.Sediment.10.12cm.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,H4,C560,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.10.12cm.R2,4,
LS_8_25_2014,LS.8.25.2014,LS_Time_Series_ABSQ_P4,I4,C553,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.25.2014,4,
Marine_Sediment_15_17cm_R1,Marine.Sediment.15.17cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,J4,C561,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.15.17cm.R1,4,
LS_1_26_2013,LS.1.26.2013,LS_Time_Series_ABSQ_P4,K4,C554,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.26.2013,4,
Marine_Sediment_20_22cm_R1,Marine.Sediment.20.22cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,L4,C562,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.20.22cm.R1,4,
LS_6_16_2014,LS.6.16.2014,LS_Time_Series_ABSQ_P4,M4,C555,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.16.2014,4,
Marine_Sediment_25_27cm_R2,Marine.Sediment.25.27cm.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,N4,C563,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.25.27cm.R2,4,
LS_7_27_2014,LS.7.27.2014,LS_Time_Series_ABSQ_P4,O4,C556,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.27.2014,4,
Marine_Sediment_30_32cm_R3,Marine.Sediment.30.32cm.R3,MarineSediment_Donor_LarrySmarr_NoProK_P5,P4,C564,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.30.32cm.R3,4,
Person_A_R3,Person.A.R3,MarineSediment_Donor_LarrySmarr_NoProK_P5,A5,C565,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.A.R3,4,
Soil_SynCom_T4_2_Tube5,Soil.SynCom.T4.2.Tube5,16_member_community_native_soil_P6,B5,C573,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T4.2.Tube5,4,
LS_9_28_2014_SRE,LS.9.28.2014.SRE,LS_Donor_SS_Samples_P1,E1,C503,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.9.28.2014.SRE,4,
Person_B_R2,Person.B.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,C5,C566,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.B.R2,4,
A21,A21,Tumor_Community_P7,D5,C574,Tellseq_Shortread_Metagenomic_Analysis_10283,A21,4,
Person_C_R4,Person.C.R4,MarineSediment_Donor_LarrySmarr_NoProK_P5,E5,C567,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.C.R4,4,
A23,A23,Tumor_Community_P7,F5,C575,Tellseq_Shortread_Metagenomic_Analysis_10283,A23,4,
Person_D_R2,Person.D.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,G5,C568,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.D.R2,4,
A27,A27,Tumor_Community_P7,H5,C576,Tellseq_Shortread_Metagenomic_Analysis_10283,A27,4,
Soil_SynCom_T1_2_Tube1,Soil.SynCom.T1.2.Tube1,16_member_community_native_soil_P6,I5,C569,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T1.2.Tube1,4,
A30,A30,Tumor_Community_P7,J5,C577,Tellseq_Shortread_Metagenomic_Analysis_10283,A30,4,
Soil_SynCom_T2_2_Tube2,Soil.SynCom.T2.2.Tube2,16_member_community_native_soil_P6,K5,C570,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T2.2.Tube2,4,
LS_7_27_2014,LS.7.27.2014,LS_Time_Series_ABSQ_P4,O4,C556,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.27.2014,4,
A31,A31,Tumor_Community_P7,L5,C578,Tellseq_Shortread_Metagenomic_Analysis_10283,A31,4,
Soil_SynCom_T3_2_Tube3,Soil.SynCom.T3.2.Tube3,16_member_community_native_soil_P6,M5,C571,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T3.2.Tube3,4,
S1_T1_A,S1.T1.A,Tumor_Community_P7,N5,C579,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.A,4,
Soil_SynCom_T4_1_Tube4,Soil.SynCom.T4.1.Tube4,16_member_community_native_soil_P6,O5,C572,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T4.1.Tube4,4,
S2_T1_B_A,S2.T1.B.A,Tumor_Community_P7,P5,C580,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.T1.B.A,4,
S2_T1_01BH1_Y_A,S2.T1.01BH1.Y.A,Tumor_Community_P7,A6,C581,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.T1.01BH1.Y.A,4,
S1_T1_1CIM_A,S1.T1.1CIM.A,Tumor_Community_P7,B6,C589,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.1CIM.A,4,
S2_MT1_1HBI_Y_A,S2.MT1.1HBI.Y.A,Tumor_Community_P7,C6,C582,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.MT1.1HBI.Y.A,4,
S1_M1_B_1CIM_A,S1.M1.B.1CIM.A,Tumor_Community_P7,D6,C590,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.M1.B.1CIM.A,4,
S1_T1_B_LBM_A,S1.T1.B.LBM.A,Tumor_Community_P7,E6,C583,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.B.LBM.A,4,
BLANK_K15_cancer_patient,BLANK.K15.cancer.patient,Tumor_Community_P7,F6,C591,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.K15.cancer.patient,4,
S2_MT1_LBM_A,S2.MT1.LBM.A,Tumor_Community_P7,G6,C584,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.MT1.LBM.A,4,
BLANK_M15_cancer_patient,BLANK.M15.cancer.patient,Tumor_Community_P7,H6,C592,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.M15.cancer.patient,4,
S2_T1_A,S2.T1.A,Tumor_Community_P7,I6,C585,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.T1.A,4,
BLANK_O15_cancer_patient,BLANK.O15.cancer.patient,Tumor_Community_P7,J6,C593,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.O15.cancer.patient,4,
1CIM_M_CNTL_A,1CIM.M.CNTL.A,Tumor_Community_P7,K6,C586,Tellseq_Shortread_Metagenomic_Analysis_10283,1CIM.M.CNTL.A,4,
BLANK_A17_cancer_patient,BLANK.A17.cancer.patient,Tumor_Community_P7,L6,C594,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.A17.cancer.patient,4,
1CIM_G_CNTL_A,1CIM.G.CNTL.A,Tumor_Community_P7,M6,C587,Tellseq_Shortread_Metagenomic_Analysis_10283,1CIM.G.CNTL.A,4,
BLANK_C17_cancer_patient,BLANK.C17.cancer.patient,Tumor_Community_P7,N6,C595,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.C17.cancer.patient,4,
GC_1HCOM_A,GC.1HCOM.A,Tumor_Community_P7,O6,C588,Tellseq_Shortread_Metagenomic_Analysis_10283,GC.1HCOM.A,4,
BLANK_E17_cancer_patient,BLANK.E17.cancer.patient,Tumor_Community_P7,P6,C596,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.E17.cancer.patient,4,
[Bioinformatics],,,,,,,,
Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,contains_replicates
Tellseq_Shortread_Metagenomic_Analysis_10283,10283,True,GATCGGAAGAGCACACGTCTGAACTCCAGTCAC,GATCGGAAGAGCGTCGTGTAGGGAAAGGAGTGT,True,Knight Lab Kapa HyperPlus,tellseq metagenomics,False
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